Microbiology spectrum最新文献

{"title":"Involvement of an orphan response regulator of the two-component regulatory system in the formation of physiologically mature sporangia in <i>Actinoplanes missouriensis</i>.","authors":"Takuya Akutsu, Zhuwen Tan, Aiko Hirata, Takeaki Tezuka, Yasuo Ohnishi","doi":"10.1128/spectrum.03272-24","DOIUrl":"10.1128/spectrum.03272-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The actinomycete &lt;i&gt;Actinoplanes missouriensis&lt;/i&gt; forms terminal sporangia that contain dormant sporangiospores. Upon contact with water, sporangia release zoospores through a process called sporangium dehiscence. In this study, we characterized &lt;i&gt;asfR&lt;/i&gt; (&lt;i&gt;AMIS_76070&lt;/i&gt;), which encodes an orphan response regulator receiver domain protein of the two-component regulatory system, as one of 136 genes whose transcription was highly activated during sporangium formation. &lt;u&gt;&lt;i&gt;A&lt;/i&gt;&lt;/u&gt;&lt;i&gt;ctinoplanes&lt;/i&gt; &lt;u&gt;s&lt;/u&gt;porangium &lt;u&gt;f&lt;/u&gt;ormation &lt;u&gt;r&lt;/u&gt;egulator (AsfR) homologs are conserved among &lt;i&gt;Actinoplanes&lt;/i&gt; bacteria. An &lt;i&gt;asfR&lt;/i&gt; null mutant (Δ&lt;i&gt;asfR&lt;/i&gt;) strain formed normally shaped sporangia containing apparently normal dormant spores, but they exhibited defective sporangium dehiscence; the number of spores released from the sporangia of the Δ&lt;i&gt;asfR&lt;/i&gt; strain was four orders of magnitude lower than that from the sporangia of the wild-type strain. This phenotypic change was recovered by introducing &lt;i&gt;asfR&lt;/i&gt; with its own promoter into the Δ&lt;i&gt;asfR&lt;/i&gt; strain. Based on the amino acid sequence and predicted structure, the function of AsfR appeared to be controlled by the phosphorylation of Asp-72. Consistently, the phenotypic change observed in the Δ&lt;i&gt;asfR&lt;/i&gt; strain was not restored by introducing a mutated &lt;i&gt;asfR&lt;/i&gt; (D72N) gene. Three orphan histidine kinases (HKs) in &lt;i&gt;A. missouriensis&lt;/i&gt; were found to interact with AsfR by screening using a bacterial two-hybrid assay. However, gene disruption experiments revealed that these three HKs were not required for sporangium dehiscence in &lt;i&gt;A. missouriensis&lt;/i&gt;. Although the molecular functions of AsfR remain to be elucidated, this study shows that AsfR is involved in the formation of physiologically mature sporangia that are fully prepared to release spores under sporangium dehiscence-inducing conditions.IMPORTANCE&lt;i&gt;Actinoplanes missouriensis&lt;/i&gt; undergoes a life cycle involving complex morphological development, including mycelial growth, sporangium formation and dehiscence, swimming as zoospores, germination, and outgrowth to mycelial growth. In this study, we revealed that a stand-alone response regulator receiver domain protein, AsfR, is required for the formation of physiologically mature sporangia that can release spores under sporangium dehiscence-inducing conditions. &lt;i&gt;A. missouriensis&lt;/i&gt; seems to express genes that are involved in sporangium dehiscence during sporangium formation, considering that an &lt;i&gt;asfR&lt;/i&gt; null mutant produced normally shaped sporangia, but these sporangia were deficient in sporangium dehiscence. Although the molecular functions of AsfR, as well as the histidine kinase(s) that phosphorylates AsfR, remain to be elucidated, identification of AsfR as a possible key regulator for the preparation of the onset and progression of sporangium dehiscence is significant, because almost no proteins involved in the early stages of sporangium dehiscence hav","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0327224"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"(p)ppGpp and DksA play a crucial role in reducing the efficacy of β-lactam antibiotics by modulating bacterial membrane permeability.","authors":"Meenal Chawla, Jyoti Verma, Shashi Kumari, Tushar Matta, Tarosi Senapati, Prabhakar Babele, Yashwant Kumar, Rupak K Bhadra, Bhabatosh Das","doi":"10.1128/spectrum.01169-24","DOIUrl":"10.1128/spectrum.01169-24","url":null,"abstract":"<p><p>The key signaling molecules in the bacterial stress-sensing pathway, the alarmone (p)ppGpp and the transcription factor DksA, play a crucial role in bacterial survival during nutritional deprivation and exposure to xenobiotics by modulating cellular metabolic pathways. In <i>Vibrio cholerae</i>, (p)ppGpp metabolism is solely linked with the functions of three proteins: RelA, SpoT, and RelV. The effects of threshold or elevated concentrations of (p)ppGpp on cellular metabolites and proteins, both in the presence and absence of DksA, have not yet been comprehensively studied in <i>V. cholerae</i> or other bacteria. We engineered the genome of <i>V. cholerae</i> to develop DksA null mutants in the presence and absence of (p)ppGpp biosynthetic enzymes. We observed that the N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>Δ<i>dksA V. cholerae</i> mutant, which lacks both (p)ppGpp and DksA, exhibits higher sensitivity to different ꞵ-lactam antibiotics compared with the wild-type (WT) strain. Our whole-cell metabolomic and proteome analysis revealed that the cell membrane and peptidoglycan biosynthesis pathways are significantly altered in the N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>, N16:Δ<i>dksA</i>, and N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>Δ<i>dksA V. cholerae</i> strains. Furthermore, the mutant strains displayed enhanced inner and outer membrane permeabilities in comparison to the WT strains. These results correlate with <i>V. cholerae's</i> tolerance and survival against β-lactam antibiotics and may inform the development of adjuvants that inhibit stringent response modulators.IMPORTANCEThe (p)ppGpp biosynthetic pathway is widely conserved in bacteria. Intracellular levels of (p)ppGpp and the transcription factor DksA play crucial roles in bacterial multiplication and viability in the presence of antibiotics and/or other xenobiotics. The present findings have shown that (p)ppGpp and DksA significantly reduce the efficacy of ꞵ-lactam and other antibiotics by modulating the availability of peptidoglycan and cell membrane-associated metabolites by reducing membrane permeability. Nevertheless, the whole-cell proteome analysis of N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>, N16:Δ<i>dksA</i>, and N16:Δ<i>relA</i>Δ<i>relV</i>Δ<i>spoT</i>Δ<i>dksA</i> strains identified the biosynthetic pathways and associated enzymes that are directly modulated by the stringent response effector molecules. Thus, the (p)ppGpp metabolic pathways and DksA could be a potential target for increasing the efficacy of antibiotics and developing antibiotic adjuvants.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0116924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CD86 immunohistochemical staining for the detection of <i>Talaromyces marneffei</i> in lesions.","authors":"Jinling Fang, Huiyuan Chen, Krishna Hamal, Donghua Liu","doi":"10.1128/spectrum.02063-24","DOIUrl":"10.1128/spectrum.02063-24","url":null,"abstract":"<p><p>Talaromycosis is an invasive fungal disease caused by the pathogenic thermodimorphic fungus <i>Talaromyces marneffei</i> (TM), which is often overlooked in tropical and subtropical regions of Asia. In view of the diversity of clinical manifestations in patients with TM infection, early diagnosis remains challenging. We assessed the sensitivity and specificity of a novel immunohistochemical staining by performing CD86 immunohistochemical staining on 56 tissue sections from patients with talaromycosis who had fungal culture or metagenomic next-generation sequencing confirmed to exist in clinical specimens, as well as 26 patients with other fungi that had been culture-proven. Hematoxylin and eosin and periodic acid Schiff (PAS) stains were also applied to each specimen. We found that anti-CD86 antibody can label TM pathogens in 38 HIV-negative specimens (38/42) and 14 HIV-positive specimens (14/14); conversely, PAS staining yielded positive results in seven cases of HIV-negative specimens (7/42) and 13 cases of HIV-positive specimens (13/14). Additionally, CD86 immunohistochemical staining was negative in other fungi. Importantly, CD86 immunohistochemical staining significantly outperformed PAS staining in terms of localizing and highlighting TM yeasts, as well as demonstrating the specificity of 100% and a significantly higher sensitivity compared to PAS staining at 92.9% versus 35.7% (<i>P</i> < 0.05, McNemar test). Our findings suggest that CD86 immunohistochemical staining has the potential for the rapid diagnosis of talaromycosis.IMPORTANCETalaromycosis is an opportunistic endemic disease without typical clinical manifestations that has emerged as a fungal disease impacting the survival and mortality of immunocompromised individuals and HIV-positive individuals in endemic regions. Nonetheless, talaromycosis is completely curable if it is accurately diagnosed and treated effectively at an early stage. Rapid pathological diagnosis relies on the unique morphological features of <i>Talaromyces marneffei</i> observed under the microscope. This study introduces a novel pathological diagnostic approach, CD86 immunohistochemical staining, to enhance the early detection of TM-infected lesions.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0206324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Peste des petits ruminants virus virulence is associated with an early inflammatory profile in the tonsils and cell cycle arrest in lymphoid tissue.","authors":"Roger-Junior Eloiflin, Llorenç Grau-Roma, Vincent Lasserre, Sylvie Python, Stephanie Talker, Philippe Totte, Obdulio García-Nicolás, Artur Summerfield, Arnaud Bataille","doi":"10.1128/spectrum.03124-24","DOIUrl":"10.1128/spectrum.03124-24","url":null,"abstract":"<p><p>Using a systems immunology approach, this study comprehensively explored the immunopathogenesis of peste des petits ruminants (PPR) focussing on strain-dependent differences in virulence. Saanen goats were infected either with the highly virulent (Morocco 2008 [MA08]) or the low-virulent (Ivory Coast 1989 [IC89]) strain of the PPR virus (PPRV). As expected, MA08-infected goats exhibited higher clinical scores, pronounced lymphocyte depletion, and lesions affecting mucosal and lymphoid tissues. CD4 T cells were more affected in terms of depletion and infection in peripheral blood. Transcriptional analyses of the blood and lymphoid tissue demonstrated activation of interferon type I (IFN-I) responses at 3 days post-infection (dpi) only with MA08, but comparable IFN-I expression levels with MA08 and IC89 at 6 dpi. MA08 strain induced strong inflammatory and myeloid cell-related transcriptional responses observed in tonsils but not in mesenteric lymph node. This inflammatory response in the tonsils was associated with an extensive damage and infection of the tonsillar epithelium in the crypts, pointing to a barrier defect as a possible cause of inflammation. An early and prominent downregulation of cell cycle gene networks was observed in all compartments analyzed in MA08-infected animals. This effect can be interpreted as suppressed lymphocyte proliferation that may cause immunosuppression during the first week following MA08 infection. A proteome analysis confirmed synthesis of IFN-I response proteins during infection with both strains, but only MA08 strain additionally upregulated ribosomal and inflammation-related proteins. In conclusion, the present comprehensive investigation delineates strain-dependent differences in early immunopathological processes associated with severe inflammation disease and a blunted lymphocyte proliferation.</p><p><strong>Importance: </strong>Field observations show that the severity of PPR is highly dependent on the viral (PPRV) strains and the host infected, but the mechanisms behind these variations are not well understood. Here we compare immune response in Saanen goats infected with high (MA08) and low (IC89) virulent PPRV strains. Analyses revealed a differential immune response: early activation of IFN-I responses only with MA08 but comparable IFN-I expression levels with MA08 and IC89 at later stages. Additionally, MA08 strain triggered inflammatory and myeloid cell-related responses in the tonsils and marked suppression of lymphocyte proliferation evidenced by cell cycle arrest. CD4 T cells were found to be most affected in terms of depletion in the peripheral blood. Massive infection of the tonsils seems to induce epithelial lesions that promote the inflammatory responses. These results underscore the need to understand strain-specific differences for PPR surveillance and control.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0312424"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143483365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics analysis of the mechanism of alfalfa and wheat-induced rumen flatulence in Xizang sheep.","authors":"Jing Wu, Xiaoming Zhang, Khan Ayesha, Shahzad Khuram, Jianzhao Cui, Gaofu Wang, Zhaxi Yangzong, Mingyan Shi, Xunping Jiang, Long Li, Guiqiong Liu, Wangsheng Zhao, Tianzeng Song","doi":"10.1128/spectrum.03268-24","DOIUrl":"10.1128/spectrum.03268-24","url":null,"abstract":"<p><p>Rumen flatulence is a diet-related rumen disease in ruminants. This study induced a rumen flatulence model in Xizang sheep using alfalfa (HRF) and wheatgrass (MRF). The aim was to understand the rumen microbiota diversity in healthy and pathological states, host-microbiota interactions, and the molecular mechanisms of rumen flatulence. Results showed that the pH in the HRF and MRF groups was lower than that in the natural grass group (LRF). SCFA concentrations varied between groups: in HRF, 2-BA and CA increased; in MRF, 4-MVA and 5-MCA rose. Microbial analysis indicated that the alpha- and beta-diversity of HRF and MRF groups were lower than LRF's, with different microbial compositions. Transcriptome analysis revealed many differentially expressed genes (DEGs). Compared to MRF, HRF had 348 upregulated and 511 downregulated DEGs. Versus LRF, MRF had 201 upregulated and 185 downregulated DEGs, while HRF had 128 upregulated and 238 downregulated DEGs. Spearman's correlation analysis showed that there was a positive correlation between <i>Butyrivibrio</i>, <i>Quinella,</i> and specific genes. These findings reveal the potential mechanism of rumen flatulence in Xizang sheep and provide new insights into the prevention and treatment of the disease.IMPORTANCEThe research used a high-protein diet to induce a model to understand the diversity of rumen microbiota and its interaction with the host, as well as exploring the molecular mechanisms of rumen flatulence.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0326824"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virus-neutralizing monoclonal antibodies against bovine viral diarrhea virus and classical swine fever virus target conformational and linear epitopes on E2 glycoprotein subdomains.","authors":"Gleyder Roman-Sosa, Denise Meyer, Mariano Dellarole, Doris À Wengen, Susanne Lerch, Alexander Postel, Paul Becher","doi":"10.1128/spectrum.02041-24","DOIUrl":"10.1128/spectrum.02041-24","url":null,"abstract":"<p><p>The envelope glycoprotein E2 of pestiviruses plays a crucial role in viral entry and elicits a virus-neutralizing humoral immune response. Consequently, the epitopes recognized by monoclonal antibodies (mAbs) on E2 are a significant focus in pestivirus research and diagnostics. In this study, we characterized a panel of murine mAbs against the E2 protein of classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV), two major pathogens for swine and cattle, respectively. The majority of mAbs neutralized the virus <i>in vitro</i> and recognized conformational epitopes, which were also detected by sera from infected animals. Notably, binding to these epitopes was retained after low-pH treatment, although conformational epitopes were disrupted upon disulfide bond reduction. The epitopes of the anti-CSFV mAbs were located in various domains of E2, including the interdomain linker sequences. Conversely, all but one of the anti-BVDV mAb epitopes were located in domain A. Moreover, the reactivity of one mAb suggests a conformational interdependence among the linker sequences of pestivirus E2. The panel of mAbs characterized in this study holds potential to support basic research on the mechanism of early pestivirus invasion and to assist in the design of E2-based diagnostic tools and vaccines.</p><p><strong>Importance: </strong>Classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV), which belong to the family Flaviviridae, cause economically significant diseases in pigs and cattle. The pestivirus glycoprotein E2 is located on the viral surface and is targeted by antibodies that neutralize virus infection. Due to its variability, E2 is a useful antigen for the development of diagnostic tests to differentiate between infections caused by different pestiviruses. In the present study, two panels of monoclonal antibodies (mAbs) specifically reactive with either CSFV or BVDV E2 were characterized. Interestingly, the majority of mAbs neutralized the respective virus <i>in vitro</i>. Epitope mapping revealed that the mAbs recognized low-pH-resistant epitopes of conformational nature located in different domains of CSFV E2 (anti-CSFV mAbs) or in domain A of BVDV E2 (anti-BVDV mAbs). The recombinant proteins along with the characterized mAbs have the potential to develop improved pestivirus-specific diagnostic tests and vaccines.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0204124"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960116/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples.","authors":"Hayden N Brochu, Qimin Zhang, Kuncheng Song, Ling Wang, Emily A Deare, Jonathan D Williams, Crystal R Icenhour, Lakshmanan K Iyer","doi":"10.1128/spectrum.02582-24","DOIUrl":"10.1128/spectrum.02582-24","url":null,"abstract":"<p><p>Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets <i>Atopobium</i> (<i>Fannyhessea</i>) <i>vaginae</i>, <i>Megasphaera-1</i>, and <i>Bacterial Vaginosis Associated Bacterium (BVAB)-2</i>. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (<i>P</i> < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct <i>Lactobacilli</i>, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0258224"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coexistence of <i>tmexCD-toprJ</i>, <i>bla</i>_NDM-1, and <i>bla</i>_PME-1 in multi-drug-resistant <i>Pseudomonas juntendi</i> isolates recovered from stool samples.","authors":"Wugao Liu, Yi Liu, Jing Jin, Ningjun Wu, Weiping Wu, Chunsheng Qu","doi":"10.1128/spectrum.01136-24","DOIUrl":"10.1128/spectrum.01136-24","url":null,"abstract":"<p><p><i>Pseudomonas juntendi</i> has received limited research attention, yet strains carrying multi-drug resistance genes pose a threat to global public health. We aimed to characterize the genome of two fecal-derived strains of <i>Pseudomonas juntendi</i>, both harboring <i>tmexCD-toprJ</i>, <i>bla</i>_NDM-1, and <i>bla</i>_PME-1 on the chromosome, recovered from two patients. Average nucleotide identity (ANI) analysis showed that L4008hy and L4046hy were remarkably similar. They showed high levels of resistance to aztreonam, imipenem, ciprofloxacin, amikacin, piperacillin-tazobactam, ceftazidime-avibactam, and polymyxin B in antimicrobial susceptibility testing using agar dilution method and broth microdilution methods. Additionally, an integrative and conjugative element (ICE) similar to ICE<i>6660</i> was detected on the chromosome, which contains all resistance genes and has a relatively complete transfer module, and potential transfer mechanisms were identified. Phylogenetic analysis of <i>P. juntendi</i> reveals the genomic diversity of the species and sheds light on environmental-human transmission.IMPORTANCEUp to now, research on <i>Pseudomonas juntendi</i> is still very limited. Our findings suggest that <i>P. juntendi</i> commonly carries diversity resistance genes on chromosomes and is stably inherited, highlighting the need for further studies on the antimicrobial properties of this bacterium. The coexistence of <i>tmexCD-toprJ</i>, <i>bla</i>_NDM-1, and <i>bla</i>_PME-1 on the chromosome in <i>P. juntendi</i> was reported for the first time. The identified integrative and conjugative element (ICE) contains all the identified resistance genes and serves as a vector for resistance gene transfer between bacteria. <i>P. juntendi</i>, which harbors multi-drug resistance genes, particularly those encoding carbapenemases, acts as a reservoir of resistance genes. Its spread in clinical settings poses additional challenges to treatment.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0113624"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960068/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-existence of plasmid-mediated <i>bla</i>_NDM-1 and <i>bla</i>_NDM-5 in <i>Escherichia coli</i> sequence type 167 and ST101 and their discrimination through restriction digestion.","authors":"Amrita Bhattacharjee, Priyanka Basak, Shravani Mitra, Jagannath Sarkar, Shanta Dutta, Sulagna Basu","doi":"10.1128/spectrum.00987-24","DOIUrl":"10.1128/spectrum.00987-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The concurrent presence of multiple New Delhi metallo-β-lactamase (&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt;) variants within an isolate often goes undetected without next-generation sequencing. This study detects and characterizes dual &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants in &lt;i&gt;Escherichia coli&lt;/i&gt; through Sanger and whole-genome sequencing. Additionally, a rapid identification method utilizing restriction digestion was designed for detecting &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants carrying M154L mutation. Antibiotic susceptibility, minimal inhibitory concentration for meropenem and ertapenem, PCR, and Sanger sequencing of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; along with genome sequencing using Illumina and Nanopore technology were conducted. Transmissibility and replicon types of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt;-harboring plasmids were evaluated. Restriction digestion using restriction enzyme, BtsCI was developed to distinguish between &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants possessing M154L mutation, such as &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-7&lt;/sub&gt; etc. Two isolates belonging to phylogroups A; ST167 and B1; ST101 and resistant to meropenem and ertapenem (≥16 mg/L) were recovered from the blood of a neonate and the rectal swab of a pregnant woman, respectively. &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; was detected by PCR, and Sanger sequences of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; showed two peaks at 262 (G and T) and 460 (A and C) nucleotide positions indicative of more than one &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variant. Hybrid assembly confirmed co-existence of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt; in each isolate. &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; was located on IncY (ST167) and IncHI1A/HI1B (ST101), while &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt; was on IncFIA/FII (ST167) and IncC (ST101) plasmids in the two isolates. Digestion with BtsC1 could discriminate between &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt;. The co-existence of multiple &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDMs&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt;, and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt; in epidemic clones of &lt;i&gt;E. coli&lt;/i&gt; is concerning. Restriction digestion method and Sanger sequencing can facilitate quick identification of dual &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants in a single isolate.IMPORTANCEThe global dissemination of antimicrobial resistance genes is a serious concern. One such gene, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt;, has spread globally via plasmids. &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; confers resistance against all β-lactam antibiotics, except monobactams. Most of the earlier literature reported the presence of single &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variant. However, this study reports the prevalence of dual &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; variants (&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt;) located on two separate plasmids identified in two distinct &lt;i&gt;Escherichia coli&lt;/i&gt; epidemic clones ST167 and ST101 isolated from a septicemic neonate and a pregnant mother, respectively. &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-5&lt;/sub&gt; differs from &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM-1&lt;/sub&gt; ","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0098724"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The tradeoffs between persistence and mutation rates at sub-inhibitory antibiotic concentrations in <i>Staphylococcus aureus</i>.","authors":"Alysha S Ismail, Brandon A Berryhill, Teresa Gil-Gil, Joshua A Manuel, Andrew P Smith, Fernando Baquero, Bruce R Levin","doi":"10.1128/spectrum.02479-24","DOIUrl":"10.1128/spectrum.02479-24","url":null,"abstract":"<p><p>The rational design of the antibiotic treatment of bacterial infections employs these drugs to reach concentrations that exceed the minimum needed to prevent the replication of the target bacteria. However, within a treated patient, spatial and physiological heterogeneity promotes antibiotic gradients such that the concentration of antibiotics at specific sites is below the minimum needed to inhibit bacterial growth. Here, we investigate the effects of sub-inhibitory antibiotic concentrations on three parameters central to bacterial infection and the success of antibiotic treatment, using <i>in vitro</i> experiments with <i>Staphylococcus aureus</i> and mathematical and computer-simulation models. Our results, using drugs of six different classes, demonstrate that exposure to sub-inhibitory antibiotic concentrations alters bacterial growth dynamics, increases the mutation rate to antibiotic resistance, and decreases the production of persister cells thereby reducing persistence levels. Understanding this trade-off between mutation rates and persistence levels resulting from sub-inhibitory antibiotic exposure is crucial for optimizing, and mitigating the failure of, antibiotic therapy.</p><p><strong>Importance: </strong>Much of the research on antibiotics and antibiotic treatment has focused on drug concentrations sufficient to prevent the growth of bacteria. These concentrations, however, are not always reached everywhere in the body. Here, we look at the effects of exposure to these low concentrations of antibiotics on the common clinically important pathogen <i>Staphylococcus aureus</i>. We confirm a previous finding that sub-inhibitory antibiotic exposure decreases the total growth and the growth rate of the bacteria. Moreover, we demonstrate that the level of persistence, an important mechanism for bacteria to survive antibiotics, is decreased due to sub-inhibitory exposure. However, we find that the rate of generation of resistant mutants is substantially increased. Taken together, these results reveal an important trade-off that emerges as a consequence of bacteria being exposed to sub-inhibitory concentrations of antibiotics.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0247924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143542543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}